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Sodium in PDB 3e8l: The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

Enzymatic activity of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

All present enzymatic activity of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins:
3.4.21.4;

Protein crystallography data

The structure of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins, PDB code: 3e8l was solved by R.Bao, C.-H.Jiang, C.W.Chi, S.X.Lin, Y.X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.48
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 76.634, 110.863, 152.991, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.5

Other elements in 3e8l:

The structure of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins (pdb code 3e8l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins, PDB code: 3e8l:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3e8l

Go back to Sodium Binding Sites List in 3e8l
Sodium binding site 1 out of 3 in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1

b:43.2
occ:1.00
N A:THR122 3.0 38.5 1.0
OG1 A:THR122 3.2 39.9 1.0
O A:HOH293 3.2 43.4 1.0
N A:SER123 3.5 40.0 1.0
O A:SER123 3.5 40.0 1.0
CG A:LYS201 3.6 37.9 1.0
NE2 A:GLN203 3.7 39.2 1.0
CA A:PRO121 3.8 38.6 1.0
CA A:THR122 3.9 39.1 1.0
C A:PRO121 3.9 38.7 1.0
OG A:SER123 3.9 41.3 1.0
CE A:LYS201 4.0 38.5 1.0
CB A:PRO121 4.0 38.6 1.0
C A:THR122 4.0 39.6 1.0
CD A:LYS201 4.1 36.8 1.0
CB A:THR122 4.1 39.1 1.0
CB A:LYS201 4.2 38.0 1.0
C A:SER123 4.3 40.2 1.0
CA A:SER123 4.4 40.1 1.0
O A:HOH275 4.6 44.1 1.0
CB A:SER123 4.7 40.0 1.0
CG2 A:THR122 4.9 38.6 1.0
CD A:GLN203 5.0 38.2 1.0

Sodium binding site 2 out of 3 in 3e8l

Go back to Sodium Binding Sites List in 3e8l
Sodium binding site 2 out of 3 in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3

b:35.0
occ:0.80
OE1 A:GLN170 2.9 43.8 1.0
O A:HOH289 2.9 31.2 1.0
OG A:SER210 3.0 37.9 0.5
O A:HOH250 3.0 29.6 1.0
CD A:GLN170 3.7 41.7 1.0
CE2 C:PHE143 3.8 27.1 1.0
NE2 A:GLN170 3.8 39.4 1.0
CH3 C:ACT181 3.8 35.0 0.8
CZ C:PHE143 3.9 27.1 1.0
CD1 A:TYR167 3.9 34.2 1.0
OG1 C:THR66 4.0 27.1 1.0
CE1 A:TYR167 4.3 34.2 1.0
CB A:SER210 4.4 37.8 0.5
CB A:SER210 4.4 37.6 0.5
CD2 C:PHE143 4.4 26.2 1.0
CE1 C:PHE143 4.6 25.7 1.0
O1 A:GOL2 4.6 35.0 0.8
OG A:SER210 4.7 36.6 0.5
CZ3 A:TRP208 4.7 36.0 1.0
C C:ACT181 4.9 35.0 0.8

Sodium binding site 3 out of 3 in 3e8l

Go back to Sodium Binding Sites List in 3e8l
Sodium binding site 3 out of 3 in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7

b:45.5
occ:1.00
CH3 A:ACT6 1.6 35.0 0.8
O A:HIS38 2.7 37.8 1.0
C A:ACT6 3.1 35.0 0.8
C A:HIS38 3.8 37.4 1.0
OXT A:ACT6 3.8 35.0 0.8
CB A:HIS38 3.9 38.2 1.0
CD1 A:TYR146 3.9 47.0 1.0
O A:ACT6 4.0 35.0 0.8
CB C:ALA147 4.1 22.5 1.0
O A:HOH269 4.1 30.2 1.0
CA A:HIS38 4.3 38.2 1.0
CD1 A:TYR37 4.3 42.8 1.0
CE1 A:TYR146 4.4 48.4 1.0
N A:HIS38 4.5 38.8 1.0
CG A:TYR146 4.5 46.2 1.0
O A:TRP136 4.7 38.3 1.0
N A:PHE39 4.8 36.6 1.0
CB A:TYR146 4.8 45.0 1.0
CE1 A:TYR37 4.9 44.5 1.0

Reference:

R.Bao, C.Z.Zhou, C.-H.Jiang, S.X.Lin, C.W.Chi, Y.X.Chen. The Ternary Structure of Double-Headed Arrowhead Protease Inhibitor Api-A Complexed with Two Trypsins Reveals A Novel Reactive Site Conformation. J.Biol.Chem. V. 284 26676 2009.
ISSN: ISSN 0021-9258
PubMed: 19640842
DOI: 10.1074/JBC.M109.022095
Page generated: Mon Oct 7 08:49:18 2024

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